Pub Date : 2024-09-08DOI: 10.1101/2024.09.05.611558
Shuang Cui, Ryutaro Furukawa, Satoshi Akanuma
For billions of years, enzymes have evolved in response to the changing environments in which their host organisms lived. Various lines of evidence suggest the earliest primitive organisms inhabited high-temperature environments and possessed enzymes adapted to such conditions. Consequently, extant mesophilic and psychrophilic enzymes are believed to have adapted to lower temperatures during the evolutionary process. Herein, we analyzed this low-temperature adaptation using ancestral sequence reconstruction. Previously, we generated the phylogenetic tree of 3-isopropylmalate dehydrogenases (IPMDHs) and reconstructed the sequence of the last bacterial common ancestor. The corresponding ancestral enzyme displayed high thermostability and catalytic activity at elevated temperatures but moderate activity at low temperatures (Furukawa et al., Sci. Rep. 10, 15493 (2020)). Here, to identify amino acid residues that are responsible for the low-temperature adaptation, we reconstructed and characterized all eleven evolutionary intermediates that sequentially connect the last bacterial common ancestor with extant mesophilic IPMDH from Escherichia coli. A remarkable change in catalytic properties, from those suited for high reaction temperatures to those adapted for low temperatures, occurred between two consecutive evolutionary intermediates. Using a combination of sequence comparisons between ancestral proteins and site-directed mutagenesis analyses, three key amino acid substitutions were identified that enhance low-temperature catalytic activity. Intriguingly, amino acid substitutions that had the most significant impact on activity at low temperatures displayed no discernable effect on thermostability. However, these substitutions markedly reduced the activation energy for catalysis, thereby improving low-temperature activity. Our findings exemplify how ancestral sequence reconstruction can identify residues crucial for adaptation to low temperatures.
{"title":"Insights into the low-temperature adaptation of an enzyme as studied through ancestral sequence reconstruction","authors":"Shuang Cui, Ryutaro Furukawa, Satoshi Akanuma","doi":"10.1101/2024.09.05.611558","DOIUrl":"https://doi.org/10.1101/2024.09.05.611558","url":null,"abstract":"For billions of years, enzymes have evolved in response to the changing environments in which their host organisms lived. Various lines of evidence suggest the earliest primitive organisms inhabited high-temperature environments and possessed enzymes adapted to such conditions. Consequently, extant mesophilic and psychrophilic enzymes are believed to have adapted to lower temperatures during the evolutionary process. Herein, we analyzed this low-temperature adaptation using ancestral sequence reconstruction. Previously, we generated the phylogenetic tree of 3-isopropylmalate dehydrogenases (IPMDHs) and reconstructed the sequence of the last bacterial common ancestor. The corresponding ancestral enzyme displayed high thermostability and catalytic activity at elevated temperatures but moderate activity at low temperatures (Furukawa et al., Sci. Rep. 10, 15493 (2020)). Here, to identify amino acid residues that are responsible for the low-temperature adaptation, we reconstructed and characterized all eleven evolutionary intermediates that sequentially connect the last bacterial common ancestor with extant mesophilic IPMDH from Escherichia coli. A remarkable change in catalytic properties, from those suited for high reaction temperatures to those adapted for low temperatures, occurred between two consecutive evolutionary intermediates. Using a combination of sequence comparisons between ancestral proteins and site-directed mutagenesis analyses, three key amino acid substitutions were identified that enhance low-temperature catalytic activity. Intriguingly, amino acid substitutions that had the most significant impact on activity at low temperatures displayed no discernable effect on thermostability. However, these substitutions markedly reduced the activation energy for catalysis, thereby improving low-temperature activity. Our findings exemplify how ancestral sequence reconstruction can identify residues crucial for adaptation to low temperatures.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-08DOI: 10.1101/2024.09.04.611248
Sharwary M R, Kunal Arekar, Praveen Karanth
Himalayan langurs (Semnopithecus schistaceus) are one of the most widely distributed colobine monkeys found in the Himalayas from Pakistan in the west to Bhutan in the east. Further, their distribution encompasses a wide range of elevation (from the foothills of the Himalayas to 4,270 m above sea level) and is interspersed with numerous deep river valleys. In this study, we investigate the role of riverine barriers and elevational gradients in shaping the population genetic structure in these langurs. Previous mitochondrial marker-based broad scale studies suggested limited role of river valleys in shaping the phylogeography of these langurs. Here we have utilized nuclear microsatellites and a more fine-scale sampling to further explore this issue. Fecal samples were non-invasively collected from two Indian Himalayan states Himachal Pradesh and Uttarakhand based on distribution records from past studies. A total of 7 microsatellite markers were genotyped for these samples. The data were subjected to various analyses, including Neighbor-joining tree, PCoA, AMOVA, STRUCTURE, and paired Mantel test. The results show an overall lack of population genetic structure and a much higher geneflow along elevational gradient than across river valleys. Significant isolation by distance was also observed. Additionally, our results do not support splitting the Himalayan langurs into multiple species/subspecies based on elevational gradient.
{"title":"Population genetics of Himalayan langurs and its taxonomic implications","authors":"Sharwary M R, Kunal Arekar, Praveen Karanth","doi":"10.1101/2024.09.04.611248","DOIUrl":"https://doi.org/10.1101/2024.09.04.611248","url":null,"abstract":"Himalayan langurs (Semnopithecus schistaceus) are one of the most widely distributed colobine monkeys found in the Himalayas from Pakistan in the west to Bhutan in the east. Further, their distribution encompasses a wide range of elevation (from the foothills of the Himalayas to 4,270 m above sea level) and is interspersed with numerous deep river valleys. In this study, we investigate the role of riverine barriers and elevational gradients in shaping the population genetic structure in these langurs. Previous mitochondrial marker-based broad scale studies suggested limited role of river valleys in shaping the phylogeography of these langurs. Here we have utilized nuclear microsatellites and a more fine-scale sampling to further explore this issue. Fecal samples were non-invasively collected from two Indian Himalayan states Himachal Pradesh and Uttarakhand based on distribution records from past studies. A total of 7 microsatellite markers were genotyped for these samples. The data were subjected to various analyses, including Neighbor-joining tree, PCoA, AMOVA, STRUCTURE, and paired Mantel test. The results show an overall lack of population genetic structure and a much higher geneflow along elevational gradient than across river valleys. Significant isolation by distance was also observed. Additionally, our results do not support splitting the Himalayan langurs into multiple species/subspecies based on elevational gradient.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-08DOI: 10.1101/2024.09.04.611314
R Keating Godfrey, Anthony Auletta, Edison Cheung, Riley M. Harper, Kireina Kates, Akito Y Kawahara, Yichen Li, Cristina Mercado, Fernando Miguelena, Ginger Pickett, Peter DiGennaro
The whitelined sphinx moth, Hyles lineata, is a generalist during both the larval and adult stages with a broad geographic range extending across North and Central America. Within the genus Hyles there have been multiple transitions to a narrower host plant range, making Hyles an ideal group to study the evolution and mechanisms of host plant selection. We characterize sex- and appendage-specific chemosensory gene expression in H. lineata, the oldest extant member of the genus. We also describe female-specific gene expression in appendages used to sense plant surfaces as a means of identifying candidate genes involved in host plant choice. Sensilla on these appendages house sensory neurons and support cells that express chemosensory genes, receptors, and small proteins that bind, shuttle, and transport small molecules to allow detection of odorants and other small molecules. We considered genes detected more frequently in the female leg and ovipositor samples to be candidate oviposition-relevant genes. Most chemosensory genes of interest were detected in both sexes, while several odorant receptors were only detected in females. We identified 18 putative chemosensory genes that were specific to female legs, ovipositors, or both body parts. However, most of these genes did not reach statistical criteria to be considered differentially expressed. Instead, a set of OBPs show statistically significant female-biased expression in legs and ovipositors. These genes may serve as candidates for future study of the evolution and mechanisms of oviposition behavior in this species and its relatives.
白刺蛾（Hyles lineata）在幼虫期和成虫期都是一种通食植物，其地理分布广泛，横跨北美洲和中美洲。在海尔斯蛾属中，寄主植物范围曾多次缩小，这使得海尔斯蛾成为研究寄主植物选择的进化和机制的理想类群。我们描述了该属现存最古老成员 H. lineata 的性别和附属器官特异性化感基因表达。我们还描述了用于感知植物表面的附肢中雌性特异性基因的表达，以此来确定参与寄主植物选择的候选基因。这些附肢上的感觉器容纳了感觉神经元和支持细胞，它们表达化学感觉基因、受体和小蛋白，这些基因、受体和小蛋白能结合、穿梭和运输小分子，从而检测气味和其他小分子。我们认为，在雌性腿部和产卵器样本中检测到的频率较高的基因是与排卵相关的候选基因。大多数感兴趣的化感基因在雌雄昆虫中都能检测到，而一些气味受体只在雌性昆虫中检测到。我们发现了 18 个对雌性腿部、产卵器或两个身体部位都有特异性的假定化感基因。然而，这些基因中的大多数都没有达到统计学标准，不能被认为是差异表达基因。相反，一组 OBPs 在腿部和产卵器中显示出显著的雌性偏向表达。这些基因可作为未来研究该物种及其近缘种产卵行为的进化和机制的候选基因。
{"title":"Sex-specific chemosensory gene expression in the whitelined sphinx moth (Lepidoptera: Hyles lineata) suggests a role for odorant-binding proteins in host plant choice","authors":"R Keating Godfrey, Anthony Auletta, Edison Cheung, Riley M. Harper, Kireina Kates, Akito Y Kawahara, Yichen Li, Cristina Mercado, Fernando Miguelena, Ginger Pickett, Peter DiGennaro","doi":"10.1101/2024.09.04.611314","DOIUrl":"https://doi.org/10.1101/2024.09.04.611314","url":null,"abstract":"The whitelined sphinx moth, Hyles lineata, is a generalist during both the larval and adult stages with a broad geographic range extending across North and Central America. Within the genus Hyles there have been multiple transitions to a narrower host plant range, making Hyles an ideal group to study the evolution and mechanisms of host plant selection. We characterize sex- and appendage-specific chemosensory gene expression in H. lineata, the oldest extant member of the genus. We also describe female-specific gene expression in appendages used to sense plant surfaces as a means of identifying candidate genes involved in host plant choice. Sensilla on these appendages house sensory neurons and support cells that express chemosensory genes, receptors, and small proteins that bind, shuttle, and transport small molecules to allow detection of odorants and other small molecules. We considered genes detected more frequently in the female leg and ovipositor samples to be candidate oviposition-relevant genes. Most chemosensory genes of interest were detected in both sexes, while several odorant receptors were only detected in females. We identified 18 putative chemosensory genes that were specific to female legs, ovipositors, or both body parts. However, most of these genes did not reach statistical criteria to be considered differentially expressed. Instead, a set of OBPs show statistically significant female-biased expression in legs and ovipositors. These genes may serve as candidates for future study of the evolution and mechanisms of oviposition behavior in this species and its relatives.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"67 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-08DOI: 10.1101/2024.09.05.611554
Zachary R Popkin-Hall, Michel A Slotman
Background: Mosquitoes in the Anopheles (An.) gambiae species complex are major vectors of Plasmodium falciparum malaria. One reason for this is the high anthropophily of the constituent species An. coluzzii, An. gambiae sensu stricto, and An. arabiensis. In contrast, their sister species An. quadriannulatus is highly zoophilic. Anopheles mosquitoes largely rely on chemical cues for host-seeking, which are primarily detected by four chemosensory gene families: olfactory receptors (Ors), ionotropic receptors (Irs), gustatory receptors (Grs), and odorant binding proteins (Obps). Genes from these families that have been implicated in host adaptation show evidence of positive selection in other insect species, including other mosquitoes. As such, we analyzed the molecular evolutionary patterns of the gustatory receptors within the Anopheles gambiae complex, with a particular interest in identifying Grs that show evidence of positive selection in highly anthropophilic species. Results: We identified sixteen Grs that show evidence of potential positive selection using the McDonald-Kreitman test, including four putative sugar receptors and two Grs with unknown ligands that are relatively highly expressed in chemosensory organs of either An. coluzzii or An. quadriannulatus. In addition, we identified twelve Grs that show evidence of potential purifying selection using the McDonald-Kreitman test, and twelve Grs that may have experienced a selective sweep using the DH test, including three putative sugar receptors and the carbon dioxide receptor Gr24. We also identified both positive and purifying selection in the coastal species An. melas (West Africa) and An. merus (East Africa). Conclusions: Our results, together with transcriptomic data, identify four Grs as possible candidates for involvement in the evolution of vertebrate host preference in the An. gambiae complex, as may have occurred in the An. farauti complex. They also point to sugar receptors as playing a role in recent adaptation of some of these species. As the vast majority of Grs have unknown functions and much is still unknown about the role of Grs in these species, a more complete interpretation of our data necessitates further characterization of these genes.
背景：冈比亚按蚊是恶性疟原虫疟疾的主要传播媒介。其原因之一是组成种群的冈比亚疟蚊（An. coluzzii）、严格意义上的冈比亚疟蚊（An. gambiae sensu stricto）和阿拉伯疟蚊（An. arabiensis）具有很高的嗜人类性。相比之下，它们的姊妹种 An. quadriannulatus 却具有很高的亲动物性。疟蚊主要依靠化学线索寻找宿主，这些线索主要由四个化学感觉基因家族检测：嗅觉受体（Ors）、离子受体（Irs）、味觉受体（Grs）和气味结合蛋白（Obps）。这些家族中与宿主适应有关的基因在其他昆虫物种（包括其他蚊子）中显示出正选择的证据。因此，我们分析了冈比亚按蚊复合体中味觉受体的分子进化模式，特别关注识别在高度嗜人类物种中显示正选择证据的 Grs：结果：通过麦克唐纳-克雷特曼检验，我们确定了 16 种显示潜在正向选择证据的 Grs，其中包括 4 种推测的糖受体和 2 种配体不明的 Grs，这些 Grs 在冈比亚疟蚊或 quadriannulatus 的化学感觉器官中的表达量相对较高。此外，我们还利用 McDonald-Kreitman 试验鉴定了 12 个显示潜在纯化选择证据的 Grs，并利用 DH 试验鉴定了 12 个可能经历了选择性横扫的 Grs，其中包括 3 个假定的糖受体和二氧化碳受体 Gr24。我们还在沿海物种 An. melas（西非）和 An. merus（东非）中发现了正选择和净化选择：我们的研究结果以及转录组数据确定了四种糖受体（Grs）可能参与了冈比亚鳗复合体对脊椎动物宿主偏好的进化，这可能也发生在法劳提鳗复合体中。他们还指出，糖受体在其中一些物种最近的适应过程中发挥了作用。由于绝大多数糖受体的功能尚不清楚，而且糖受体在这些物种中的作用仍有许多未知之处，因此要对我们的数据进行更全面的解释，就必须进一步确定这些基因的特征。
{"title":"Molecular Evolution of Gustatory Receptors in the Anopheles gambiae Species Complex","authors":"Zachary R Popkin-Hall, Michel A Slotman","doi":"10.1101/2024.09.05.611554","DOIUrl":"https://doi.org/10.1101/2024.09.05.611554","url":null,"abstract":"Background: Mosquitoes in the Anopheles (An.) gambiae species complex are major vectors of Plasmodium falciparum malaria. One reason for this is the high anthropophily of the constituent species An. coluzzii, An. gambiae sensu stricto, and An. arabiensis. In contrast, their sister species An. quadriannulatus is highly zoophilic. Anopheles mosquitoes largely rely on chemical cues for host-seeking, which are primarily detected by four chemosensory gene families: olfactory receptors (Ors), ionotropic receptors (Irs), gustatory receptors (Grs), and odorant binding proteins (Obps). Genes from these families that have been implicated in host adaptation show evidence of positive selection in other insect species, including other mosquitoes. As such, we analyzed the molecular evolutionary patterns of the gustatory receptors within the Anopheles gambiae complex, with a particular interest in identifying Grs that show evidence of positive selection in highly anthropophilic species.\u0000Results: We identified sixteen Grs that show evidence of potential positive selection using the McDonald-Kreitman test, including four putative sugar receptors and two Grs with unknown ligands that are relatively highly expressed in chemosensory organs of either An. coluzzii or An. quadriannulatus. In addition, we identified twelve Grs that show evidence of potential purifying selection using the McDonald-Kreitman test, and twelve Grs that may have experienced a selective sweep using the DH test, including three putative sugar receptors and the carbon dioxide receptor Gr24. We also identified both positive and purifying selection in the coastal species An. melas (West Africa) and An. merus (East Africa).\u0000Conclusions: Our results, together with transcriptomic data, identify four Grs as possible candidates for involvement in the evolution of vertebrate host preference in the An. gambiae complex, as may have occurred in the An. farauti complex. They also point to sugar receptors as playing a role in recent adaptation of some of these species. As the vast majority of Grs have unknown functions and much is still unknown about the role of Grs in these species, a more complete interpretation of our data necessitates further characterization of these genes.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-08DOI: 10.1101/2024.09.04.611184
Thibault Leroy, Pierre Faux, Benjamin Basso, Sonia Eynard, David Wragg, Alain Vignal
Bees are vital pollinators in natural and agricultural landscapes around the globe, playing a key role in maintaining flowering plant biodiversity and ensuring food security. Among the honey bee species, the Western honey bee (Apis mellifera) is particularly significant, not only for its extensive crop pollination services but also for producing economically valuable products such as honey. Here, we analyzed whole-genome sequence data from four Apis species to explore how honey bee evolution has shaped current diversity patterns. Using Approximate Bayesian Computation, we first reconstructed the demographic history of A. mellifera in Europe, finding support for postglacial secondary contacts, therefore predating human-mediated transfers linked to modern beekeeping. However, our analysis of recent demographic changes then reveals significant bottlenecks due to beekeeping practices, which have notably affected genetic diversity. Black honey bee populations from conservatories, particularly those on islands, exhibit considerable genetic loss, raising concerns about the long-term effectiveness of current conservation strategies. Additionally, we observed a high degree of conservation in the genomic landscapes of nucleotide diversity across the four species, despite a divergence gradient spanning over 15 million years, consistent with a long-term conservation of the recombination landscapes. Taken together, our results provide the most comprehensive assessment of diversity patterns in honey bees to date and offer insights into the optimal management of resources to ensure the long-term persistence of honey bees and their invaluable pollination services.
{"title":"Inferring long-term and short-term determinants of genetic diversity in honey bees: Beekeeping impact and conservation strategies","authors":"Thibault Leroy, Pierre Faux, Benjamin Basso, Sonia Eynard, David Wragg, Alain Vignal","doi":"10.1101/2024.09.04.611184","DOIUrl":"https://doi.org/10.1101/2024.09.04.611184","url":null,"abstract":"Bees are vital pollinators in natural and agricultural landscapes around the globe, playing a key role in maintaining flowering plant biodiversity and ensuring food security. Among the honey bee species, the Western honey bee (Apis mellifera) is particularly significant, not only for its extensive crop pollination services but also for producing economically valuable products such as honey. Here, we analyzed whole-genome sequence data from four Apis species to explore how honey bee evolution has shaped current diversity patterns. Using Approximate Bayesian Computation, we first reconstructed the demographic history of A. mellifera in Europe, finding support for postglacial secondary contacts, therefore predating human-mediated transfers linked to modern beekeeping. However, our analysis of recent demographic changes then reveals significant bottlenecks due to beekeeping practices, which have notably affected genetic diversity. Black honey bee populations from conservatories, particularly those on islands, exhibit considerable genetic loss, raising concerns about the long-term effectiveness of current conservation strategies. Additionally, we observed a high degree of conservation in the genomic landscapes of nucleotide diversity across the four species, despite a divergence gradient spanning over 15 million years, consistent with a long-term conservation of the recombination landscapes. Taken together, our results provide the most comprehensive assessment of diversity patterns in honey bees to date and offer insights into the optimal management of resources to ensure the long-term persistence of honey bees and their invaluable pollination services.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"80 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-08DOI: 10.1101/2024.09.05.611460
Petra G. Simkova, Viktoria A. Krenn, Cinzia Fornai, Lisa Wurm, Vanda Halasz, Dominika Lidinsky, Gerhard W. Weber
Morphological covariation within the modern human postcanine dentition remains an open field of study. Analysis of covariation patterns of the three-dimensional (3D) shape between different tooth types has been seldom conducted, but it is relevant for the advancement of human biology and evolution, as well as dental anthropology, phylogeny, and medicine. Here, we analysed 3D shape covariation of the postcanine dentition (excluding third molars), both within and between dental arches using geometric morphometrics (GM). Based on high-resolution (micro-CT) scans of 526 teeth from 136 individuals we found high pairwise correlation in tooth pairs within the dental arches (lower P3 and P4, r1 = 0.89; upper P3 and P4, r1 = 0.81; upper M1 and M2, r1 = 0.86). The correlation values between antagonists varied notably from the highest value detected between upper and lower M1s (r = 0.9), to the lowest between upper P4s and lower M1s (r = 0.58). Of all analysed tooth types, only the upper M1s showed moderate to high correlation in every pair analysis. Noticeably, unusually high covariation was detected between some of the tooth type pairs that do not articulate in a normal dentition (e.g., lower P3 and upper M2, r1 = 0.88). Furthermore, a relatively high covariation was found in the pairs of lower P4s and M1s (r1 = 0.79), and upper P4s and M1s (r1 = 0.77), which are the only tooth type pairs of the postcanine dentition belonging to different tooth classes (premolars and molars, respectively) and still serving similar masticatory functions. This study points to the fact that higher morphological integration seems to characterize teeth within the same dental arch rather than between antagonistic teeth. With this study, we provided an overview of pairwise correlations and strength of covariation between different tooth types. This information might inform future studies aimed at understanding developmental, phylogenetic, and functional aspects of the human postcanine dentition, including possible phenotype-genotype associations. However, with this study being the first one performed on a 3D sample of this size, we also report on obstacles and peculiarities that have been determined.
{"title":"Connecting crowns: Analyzing morphological covariation in the modern human postcanine dentition","authors":"Petra G. Simkova, Viktoria A. Krenn, Cinzia Fornai, Lisa Wurm, Vanda Halasz, Dominika Lidinsky, Gerhard W. Weber","doi":"10.1101/2024.09.05.611460","DOIUrl":"https://doi.org/10.1101/2024.09.05.611460","url":null,"abstract":"Morphological covariation within the modern human postcanine dentition remains an open field of study. Analysis of covariation patterns of the three-dimensional (3D) shape between different tooth types has been seldom conducted, but it is relevant for the advancement of human biology and evolution, as well as dental anthropology, phylogeny, and medicine. Here, we analysed 3D shape covariation of the postcanine dentition (excluding third molars), both within and between dental arches using geometric morphometrics (GM). Based on high-resolution (micro-CT) scans of 526 teeth from 136 individuals we found high pairwise correlation in tooth pairs within the dental arches (lower P3 and P4, r1 = 0.89; upper P3 and P4, r1 = 0.81; upper M1 and M2, r1 = 0.86). The correlation values between antagonists varied notably from the highest value detected between upper and lower M1s (r = 0.9), to the lowest between upper P4s and lower M1s (r = 0.58). Of all analysed tooth types, only the upper M1s showed moderate to high correlation in every pair analysis. Noticeably, unusually high covariation was detected between some of the tooth type pairs that do not articulate in a normal dentition (e.g., lower P3 and upper M2, r1 = 0.88). Furthermore, a relatively high covariation was found in the pairs of lower P4s and M1s (r1 = 0.79), and upper P4s and M1s (r1 = 0.77), which are the only tooth type pairs of the postcanine dentition belonging to different tooth classes (premolars and molars, respectively) and still serving similar masticatory functions.\u0000This study points to the fact that higher morphological integration seems to characterize teeth within the same dental arch rather than between antagonistic teeth. With this study, we provided an overview of pairwise correlations and strength of covariation between different tooth types. This information might inform future studies aimed at understanding developmental, phylogenetic, and functional aspects of the human postcanine dentition, including possible phenotype-genotype associations. However, with this study being the first one performed on a 3D sample of this size, we also report on obstacles and peculiarities that have been determined.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Understanding the structural changes that enable enzymes to remain active in extreme thermal conditions is of broad scientific interest for both fundamental and applied biological research. Three commonly discussed mechanisms that underlie the thermal adaptation of enzymes include modifications in structural flexibility, compactness, and in the contact network among amino acids. However, most previous studies on these topics have been limited to small sample sizes or a narrow taxonomic focus, and the relative importance of these factors to thermal adaptation remains poorly understood. In this study, we combined molecular dynamics simulations and phylogenetic comparative analyses to thoroughly analyse the structural factors underlying thermal adaptation across 70 prokaryotic adenylate kinases, a key enzyme involved in cellular energy balance and homeostasis. We detect systematic increases in the flexibility of the enzyme with temperature, both across and within species. In contrast, structural compactness appears to be almost completely independent of temperature. Finally, we detect a remarkable diversity in the contact networks of different adenylate kinases that cannot be explained solely by temperature. Our results suggest that there are multiple paths toward the adaptation of prokaryotic adenylate kinases to extreme thermal environments, but such paths generally involve changes in flexibility.
{"title":"Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases","authors":"Dimitrios - Georgios Kontopoulos, Ilias Patmanidis, Timothy G. Barraclough, Samraat Pawar","doi":"10.1101/2024.09.04.611173","DOIUrl":"https://doi.org/10.1101/2024.09.04.611173","url":null,"abstract":"Understanding the structural changes that enable enzymes to remain active in extreme thermal conditions is of broad scientific interest for both fundamental and applied biological research. Three commonly discussed mechanisms that underlie the thermal adaptation of enzymes include modifications in structural flexibility, compactness, and in the contact network among amino acids. However, most previous studies on these topics have been limited to small sample sizes or a narrow taxonomic focus, and the relative importance of these factors to thermal adaptation remains poorly understood. In this study, we combined molecular dynamics simulations and phylogenetic comparative analyses to thoroughly analyse the structural factors underlying thermal adaptation across 70 prokaryotic adenylate kinases, a key enzyme involved in cellular energy balance and homeostasis. We detect systematic increases in the flexibility of the enzyme with temperature, both across and within species. In contrast, structural compactness appears to be almost completely independent of temperature. Finally, we detect a remarkable diversity in the contact networks of different adenylate kinases that cannot be explained solely by temperature. Our results suggest that there are multiple paths toward the adaptation of prokaryotic adenylate kinases to extreme thermal environments, but such paths generally involve changes in flexibility.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-08DOI: 10.1101/2024.09.03.610719
Peter J Waddell, Remco R Bouckaert
The combination of a time reversible Markov process with a 'hidden' mixture of gamma distributed relative site rates plus invariant sites have become the most favoured options for likelihood and other probabilistic models of nucleotide evolution (e.g., tr4gi which approximates a gamma with four rate classes). However, these models assume a homogeneous and stationary distribution of nucleotide (character or base) frequencies. Here, we explore the potential benefits and pitfalls of allowing each rate category (rate class) of a 4gi mixture model to have its own base frequencies. This is achieved by starting each of the five rate classes, at the tree's root, with its own free choice of nucleotide frequencies to create a 4gi5rf model or a 5rf model in shorthand We assess the practical identifiability of this approach with a BEAST 2 implementation, aiming to determine if it can accurately estimate credibility intervals and expected values for a wide range of plausible parameter values. Practical identifiability, as distinguished from mathematical identifiability, gauges the model's ability to identify parameters in real-world scenarios, as opposed to theoretically with infinite data. One of the most common types of phylogenetic data is mitochondrial DNA (mtDNA) protein coding sequence. It is often assumed current models analyse robustly such data and that higher likelihood/posterior probability models do better. However, this abstract shows that vertebrate mtDNA remains a very difficult type of data to fully model, and that dramatically higher likelihoods do not mean a model is measurably more accurate with respect to recovering key parameters of biological interest (e.g., monophyletic groups, their support and their ages). The 4gi5rf model considerably improves marginal likelihoods and seems to reverse some apparent errors exacerbated by the 4gi model, while introducing others. Problems appear to be linked to non-stationary DNA repair processes that alter the mutation/substitution spectra across lineages and time. We also show such problems are not unique to mtDNA and are encountered in analysing nuclear sequences. Non-stationarity of DNA repair processes mutation/substitution spectra thus pose an active challenge to obtaining reliable inferences of relationships and divergence times near the root of placental mammals, for example. An open source implementation is available under the LGPL 3.0 license in the beastbooster package for BEAST 2, available from https://github.com/rbouckaert/beastbooster.
{"title":"An independent base composition of each rate class for improved likelihood-based phylogeny estimation: The 5rf model","authors":"Peter J Waddell, Remco R Bouckaert","doi":"10.1101/2024.09.03.610719","DOIUrl":"https://doi.org/10.1101/2024.09.03.610719","url":null,"abstract":"The combination of a time reversible Markov process with a 'hidden' mixture of gamma distributed relative site rates plus invariant sites have become the most favoured options for likelihood and other probabilistic models of nucleotide evolution (e.g., tr4gi which approximates a gamma with four rate classes). However, these models assume a homogeneous and stationary distribution of nucleotide (character or base) frequencies. Here, we explore the potential benefits and pitfalls of allowing each rate category (rate class) of a 4gi mixture model to have its own base frequencies. This is achieved by starting each of the five rate classes, at the tree's root, with its own free choice of nucleotide frequencies to create a 4gi5rf model or a 5rf model in shorthand We assess the practical identifiability of this approach with a BEAST 2 implementation, aiming to determine if it can accurately estimate credibility intervals and expected values for a wide range of plausible parameter values. Practical identifiability, as distinguished from mathematical identifiability, gauges the model's ability to identify parameters in real-world scenarios, as opposed to theoretically with infinite data. One of the most common types of phylogenetic data is mitochondrial DNA (mtDNA) protein coding sequence. It is often assumed current models analyse robustly such data and that higher likelihood/posterior probability models do better. However, this abstract shows that vertebrate mtDNA remains a very difficult type of data to fully model, and that dramatically higher likelihoods do not mean a model is measurably more accurate with respect to recovering key parameters of biological interest (e.g., monophyletic groups, their support and their ages). The 4gi5rf model considerably improves marginal likelihoods and seems to reverse some apparent errors exacerbated by the 4gi model, while introducing others. Problems appear to be linked to non-stationary DNA repair processes that alter the mutation/substitution spectra across lineages and time. We also show such problems are not unique to mtDNA and are encountered in analysing nuclear sequences. Non-stationarity of DNA repair processes mutation/substitution spectra thus pose an active challenge to obtaining reliable inferences of relationships and divergence times near the root of placental mammals, for example. An open source implementation is available under the LGPL 3.0 license in the beastbooster package for BEAST 2, available from https://github.com/rbouckaert/beastbooster.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-08DOI: 10.1101/2024.09.06.611503
Rahul Unni, Onur Erk Kavlak, Eva H. Stukenbrock, Primrose J. Boynton
Endosymbioses, the intimate relationships between smaller symbionts and larger hosts, have profound impacts on eukaryotic organisms. However, symbiont effects on host fitness in natural conditions are difficult to study, especially for microbial hosts. We used killer viruses and the wild yeast Saccharomyces paradoxus to study a symbiotic virus's effect on its host's fitness in oak litter. We cured hosts of naturally-occurring killer viruses and compared killer and cured individuals' fitnesses in laboratory medium and oak litter using a unique field chamber design to house competing S. paradoxus. In the laboratory, the impact of virus loss on host fitness could be positive, negative, or neutral, depending on host identity. Trends in the forest were similar to those in the lab, although only overall strain fitness differences were significant and curing impacts differed between the forest and laboratory. These results demonstrate the importance of incorporating environmental context into studies of host-symbiont interactions.
{"title":"Fitness effects of killer virus infection on wild Saccharomyces paradoxus","authors":"Rahul Unni, Onur Erk Kavlak, Eva H. Stukenbrock, Primrose J. Boynton","doi":"10.1101/2024.09.06.611503","DOIUrl":"https://doi.org/10.1101/2024.09.06.611503","url":null,"abstract":"Endosymbioses, the intimate relationships between smaller symbionts and larger hosts, have profound impacts on eukaryotic organisms. However, symbiont effects on host fitness in natural conditions are difficult to study, especially for microbial hosts. We used killer viruses and the wild yeast <em>Saccharomyces paradoxus</em> to study a symbiotic virus's effect on its host's fitness in oak litter. We cured hosts of naturally-occurring killer viruses and compared killer and cured individuals' fitnesses in laboratory medium and oak litter using a unique field chamber design to house competing <em>S. paradoxus</em>. In the laboratory, the impact of virus loss on host fitness could be positive, negative, or neutral, depending on host identity. Trends in the forest were similar to those in the lab, although only overall strain fitness differences were significant and curing impacts differed between the forest and laboratory. These results demonstrate the importance of incorporating environmental context into studies of host-symbiont interactions.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-07DOI: 10.1101/2024.09.03.611045
Jesse B Borden, James Gibbs, John P Vanek, Bradley Cosentino
Urbanization, as the fastest growing land use type, shapes biodiversity through a suite of abiotic and biotic changes driven by the profound alteration of environmental conditions in built environments. Understanding the mechanisms behind biodiversity patterns in urban areas requires disentangling the direct and indirect pathways through which urbanization impacts ecological and evolutionary dynamics. We show how a structural causal modeling framework can be used to provide insight into processes generating biodiversity patterns in urban contexts by building structural equation models to disentangle direct and indirect pathways by which urbanization affects abundance and coat color variation in eastern gray squirrels (Sciurus carolinensis). Integrating camera traps and point count surveys across 49 sites, we observed pronounced urban-rural gradients in squirrel abundance and color variation. Human population density affected abundance of color morphs by mediating resource availability, predator activity, habitat amount, and fragmentation. But markedly different mechanisms drove abundance of color morphs across the landscape. Our findings reveal how explicit modeling of multiple pathways of environmental change can deepen our mechanistic understanding of how urbanization alters biodiversity patterns.
{"title":"Ecological and evolutionary impacts of urbanization: applying a causal modeling framework","authors":"Jesse B Borden, James Gibbs, John P Vanek, Bradley Cosentino","doi":"10.1101/2024.09.03.611045","DOIUrl":"https://doi.org/10.1101/2024.09.03.611045","url":null,"abstract":"Urbanization, as the fastest growing land use type, shapes biodiversity through a suite of abiotic and biotic changes driven by the profound alteration of environmental conditions in built environments. Understanding the mechanisms behind biodiversity patterns in urban areas requires disentangling the direct and indirect pathways through which urbanization impacts ecological and evolutionary dynamics. We show how a structural causal modeling framework can be used to provide insight into processes generating biodiversity patterns in urban contexts by building structural equation models to disentangle direct and indirect pathways by which urbanization affects abundance and coat color variation in eastern gray squirrels (Sciurus carolinensis). Integrating camera traps and point count surveys across 49 sites, we observed pronounced urban-rural gradients in squirrel abundance and color variation. Human population density affected abundance of color morphs by mediating resource availability, predator activity, habitat amount, and fragmentation. But markedly different mechanisms drove abundance of color morphs across the landscape. Our findings reveal how explicit modeling of multiple pathways of environmental change can deepen our mechanistic understanding of how urbanization alters biodiversity patterns.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"67 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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